Cheap designer genes

The kind of DNA-based nanotechnology pioneered by New York University’s Ned Seeman is currently the closest thing we have to the radical aim of making nanoscale structures and machines with atomic precision, but the development of the technology is limited by cost. DNA is an expensive molecule – currently it costs about $5000 a gram to make short, synthetic DNA sequences.

It’s not DNA nanotechnology that the company cites as its major potential market, though. Their ambition is to make synthetic genes for synthetic organisms, in the emerging field of synthetic biology.

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on Monday, August 15th, 2005 at 12:53 pm and is filed under Bio-nanotechnology, General.
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12 Responses to “Cheap designer genes”

Yeah, synthetic biology is the real nanotechnology (will the real nanotech please self-assemble).
Unless someone can convince me otherwise, I do not believe that a general purpose self-assembly based on “dry” nanotech (mechano-synthesis) is possible. Even if it is possible, “wet” nanotech is better because it occurs at room temperature and pressure in an aqueous environment. The solute-solvent chemistry is so varied and capabile, I find it difficult that vacuum-based “dry” nanotech can effectively compete with it in producing the wide variety of materials and structures found in biology (and industry) today. So, for true autonomous, self-assembly manufacturing, we are left with synthetic biology.

Perhaps it is likely that several versions of synthetic biology will be developed, each optimized for making specific products or structures. There are people at Los Alamos who are working with a polymer replacement to DNA, called PNA. I know that there are research groups all over the world trying to develop tsynthetic biology.

Kurt,
“Unless someone can convince me otherwise, I do not believe that a general purpose self-assembly based on ‚Äúdry‚Äù nanotech (mechano-synthesis) is possible”

One small point first, “dry” nanotech is not trying to use self-assembly it is trying to use directed or positional assembly.

If you go to Eric Drexler’s site http://e-drexler.com/
look at the paper he wrote with Damian Allis, “Design and Analysis of a Molecular Tool for Carbon Transfer in Mechanosynthesis. ” The paper describes what should be a very reliable tool tip for making diamond and graphite structures.

I think the paper answers three important objections that have been made about “drexlerian” nanotechnology. It shows that the “fat fingers” and “sticky fingers” problems can be overcome with the right design (and if you limit what you build to diamond and graphite like structures.) The paper also gives chemists a synthetic target to shoot for (the tool tip).

Drexler’s paper is theoretical. His proposal may or may not work. I would like to see experimental work verifying that such directed assembly on the molecular level. I have yet to see this.

The other issue is scaling. Can large macroscopic systems be made by scaling up such mechanosynthesis? I’m not saying that Drexler is wrong. Its just at this point in time, “wet” nanotechnology looks alot more feasible, especially in the near term (next 20 years).

Another point worth making about the Drexler/Allis paper is that it concentrates on the molecular design for the tool-tip, and implicitly assumes that it’s going to be possible to make a pyrimidal tool to stick the tip on the end of. Which, of course, is perfectly possible in principle, but there seems no clear way of implementing this in practise at the moment. The same point was extensively discussed by Philip Moriarty in the context of his critique of the Freitas proposal for diamond mechanosynthesis.

I am convinced that BOTH “dry” and “wet” MNT make sense. But here is my main question to the bio nano people:

Can we use wet nanotech to DIRECTLY build HARD, Dry, Covalent structures, like diamond, fullerene nanotubes, metals, ceramics, and other structures, covalent polymers, or not? The strength and hardness and toughness of materials is what counts in materials synthesis. Bone is nice, and amazing, and a miraculous substance, but bone and shell and these structures are inherently weak because of their STARTING MATERIALS. If we used molecular layered covalent structures and assembled them in the same structures or similiar structures, or better structures than we see in nature, we are on the right track. Can this be done with Bio Engineering or do we NEED Mechanosynthesis?

Good question. Self-assembly almost by definition involves weak bonds, so on the face of it no self-assembled material can be very strong or stiff. To get round this, there are a number of approaches used by nature and increasingly by materials scientists. You can build a nanostructured material by using a soft self-assembled structure to template the growth of a hard, covalent material. Jeff Brinker at Sandia is a pioneer of this approach. Or you can make a relatively weak precursor structure by self-assembly, which you subsequently post-process to produce something much stronger. This is how tendon is made, for example; the way commercial carbon fibre is made is a crude version of the process. Lots of materials scientists are studying spider silk, which can be very strong and tough indeed.

The latter idea referencing tendons: how large would such a self-assembled structure have to be (in nm) before it could be post-processed to make strong building blocks? Would the processing be possible using our existing library of materials engineering techniques? Thx.

If you are using a macromolecule as a building block, it needs to be reasonably long. This is for two reasons; firstly if you want what you make to be stiff and strong you need to pull the molecule out straight so you are directly pulling on the carbon-carbon bonds, and it turns out to be easier to do this for longer bits of string than shorter ones. Then you need a reasonable length to bind the sheaf of bits of string together, as it were. How long do you need? Depends on the system, I suppose, but I’d guess you usually need many tens to a few hundred repeating units, i.e. say a few tens of nm. There are certainly some useful things to do with existing techniques or developments of them, but there’s certainly room for new processes and new chemistry.

I think it’s too early for there to be a book on synthetic biology. This web-site has pointers to lots of good resources, though. (Worth mentioning also that I found this from Martyn Amos’s blog, which covers synthetic biology amongst other interesting topics)>

Another good synthetic bio site is OpenWetWare. Like syntheticbiology.org, it’s run by the MIT crowd. This is emerging as an open forum for researchers and the public. There are some other related links you might find interesting at the bottom of a post I wrote on synthetic biology.